public Color getBackgroundBoxColor() {
if (pos == targetNucleotide && tier == targetTier) return targetColor;
int lowSeqSelect;
int highSeqSelect;
if (baseEditor instanceof BaseEditorPanel) {
lowSeqSelect = ((BaseEditorPanel) baseEditor).selectLowPos();
highSeqSelect = ((BaseEditorPanel) baseEditor).selectHighPos();
} else {
lowSeqSelect = -1;
highSeqSelect = -1;
}
if (lowSeqSelect != -1 && highSeqSelect != -1 && pos >= lowSeqSelect && pos <= highSeqSelect) {
return seqSelectColor;
}
int basePos = baseEditor.posToBasePair(pos);
if (((BaseEditorPanel) baseEditor).isSequencingErrorPosition(basePos)) return shiftColor;
if (isExon) {
ExonI exon = null;
if (currentFeature instanceof ExonI) exon = (ExonI) currentFeature;
else if (currentFeature instanceof DrawableSeqFeature)
exon = (ExonI) ((DrawableSeqFeature) currentFeature).getFeature();
if (exon != null && exon.getTranscript() != null) {
Transcript transcript = exon.getTranscript();
int tss = (int) exon.getTranscript().getTranslationStart();
if (basePos == tss
|| basePos == (tss + exon.getStrand())
|| basePos == (tss + (2 * exon.getStrand())))
return DrawableUtil.getStartCodonColor(transcript);
else {
int tes = (int) transcript.getTranslationEnd();
if (basePos == tes
|| basePos == (tes + exon.getStrand())
|| basePos == (tes + (2 * exon.getStrand()))) return Color.red;
else {
int shift_pos = (int) transcript.plus1FrameShiftPosition();
if (basePos == shift_pos) return shiftColor;
else {
shift_pos = (int) transcript.minus1FrameShiftPosition();
if (basePos == shift_pos) return shiftColor;
else {
int stop_pos = (int) transcript.readThroughStopPosition();
if (basePos == stop_pos
|| basePos == (stop_pos + exon.getStrand())
|| basePos == (stop_pos + (2 * exon.getStrand()))) return Color.pink;
}
}
}
}
}
return transcriptColorList[transcriptColorIndex][exonColorIndex];
}
return null;
}
